Today I did not have invitory space to collect my faction package and under the assumption that I would still receive one via mail or New Monarchy themselves, I continued to turn in material for xp like a dork. Well, I lost two packages in the process. I don't know if this is a bug or if this is an update that I missed along the way. Is there any way I can get a refund of two packages or was it completely my bad? I will definitely pay more attention in the future, that's for sure.
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Unfortunately there is nothing that can be done at this point. As you found out, packages no longer go to the postmaster. They now need to be picked up from the faction quartermaster. Levelling a faction up again before picking up the package will overwrite the first package. https://www.bungie.net/en/Help/Article/13480